Directory listing for /

• .claude/
• .gitignore
• .progress.lock
• .qc_progress.lock
• analyze_gwas_metrics.R
• assessment_centre_phenotypes-columns.csv
• assessment_centre_phenotypes_stats.tsv
• clinical_phenotypes_stats.tsv
• combined_all_variants_manhattan.png
• combined_all_variants_manhattan_effect_combined.png
• combined_all_variants_qq_full.png
• combined_all_variants_qq_zoom.png
• combined_all_variants_snv_only_qq_full.png
• combined_all_variants_snv_only_qq_zoom.png
• combined_all_variants_snv_qq_by_chr.png
• contingency_A099.tsv
• contingency_A419.tsv
• contingency_acamprosate__longest_therapy_duration.tsv
• contingency_acamprosate__longest_therapy_duration__ln.tsv
• contingency_acamprosate__max_dose.tsv
• contingency_acamprosate__max_dose__ln.tsv
• contingency_acamprosate__mean_dose.tsv
• contingency_acamprosate__mean_dose__ln.tsv
• contingency_acamprosate__median_dose.tsv
• contingency_acamprosate__median_dose__ln.tsv
• contingency_all.py
• contingency_amitriptyline__M255.tsv
• contingency_amlodipine__I500.tsv
• contingency_amlodipine__K922.tsv
• contingency_amlodipine__M796.tsv
• contingency_amlodipine__optimal_dose.tsv
• contingency_amlodipine__R060.tsv
• contingency_amlodipine__Z958.tsv
• contingency_apomorphine__max_dose.tsv
• contingency_atenolol__M549.tsv
• contingency_atenolol__N920.tsv
• contingency_atenolol__R739.tsv
• contingency_atorvastatin__F419.tsv
• contingency_atorvastatin__K20.tsv
• contingency_atorvastatin__K30.tsv
• contingency_atorvastatin__K760.tsv
• contingency_atorvastatin__optimal_dose__ln.tsv
• contingency_atorvastatin__R53.tsv
• contingency_atorvastatin__R634.tsv
• contingency_batch.log
• contingency_bisoprolol__A419.tsv
• contingency_buprenorphine__num_of_prescriptions.tsv
• contingency_chlorpromazine__mean_dose.tsv
• contingency_citalopram__I209.tsv
• contingency_citalopram__R634.tsv
• contingency_citalopram__Z966.tsv
• contingency_clopidogrel__L988.tsv
• contingency_diltiazem__K602.tsv
• contingency_fentanyl__prescribed.tsv
• contingency_fluoxetine__R53.tsv
• contingency_full_test.log
• contingency_furosemide__E162.tsv
• contingency_furosemide__K922.tsv
• contingency_gabapentin__A419.tsv
• contingency_gabapentin__R42.tsv
• contingency_glyceryl_trinitrate__optimal_dose.tsv
• contingency_ibuprofen__optimal_dose.tsv
• contingency_jobs_morphine__E86/
• contingency_jobs_morphine__I48/
• contingency_jobs_morphine__J189/
• contingency_jobs_simvastatin__J069/
• contingency_jobs_tramadol__L409/
• contingency_jobs_zopiclone__G470/
• contingency_jobs_zopiclone__M796/
• contingency_L570.tsv
• contingency_losartan__L089.tsv
• contingency_morphine__E86.tsv
• contingency_morphine__I48.tsv
• contingency_morphine__J189.tsv
• contingency_morphine__optimal_dose.tsv
• contingency_nicorandil__prescribed.tsv
• contingency_olmesartan__num_of_therapies.tsv
• contingency_olmesartan__prescribed.tsv
• contingency_oxazepam__longest_therapy_duration.tsv
• contingency_p1558_i0__alcohol_intake_freq.tsv
• contingency_p1727_i0_ohe1__skin_tan_ease__very_tan.tsv
• contingency_p2188_i0__long_illness.tsv
• contingency_p23436_i0__cholines_total.tsv
• contingency_p23461_i0__glutamine.tsv
• contingency_p23468_i0__phenylalanine.tsv
• contingency_p23471_i0__lactate.tsv
• contingency_p30780_i0__ldl_direct.tsv
• contingency_p48_i0__waist_circ.tsv
• contingency_pethidine__longest_therapy_duration.tsv
• contingency_prasugrel__num_of_therapies.tsv
• contingency_pregabalin__M139.tsv
• contingency_propranolol__median_dose__ln.tsv
• contingency_propranolol__prescribed.tsv
• contingency_ramipril__A099.tsv
• contingency_ramipril__I10.tsv
• contingency_ramipril__I951.tsv
• contingency_ramipril__L409.tsv
• contingency_ramipril__R410.tsv
• contingency_rosuvastatin__optimal_dose.tsv
• contingency_runner.sh
• contingency_simvastatin__I10.tsv
• contingency_simvastatin__I802.tsv
• contingency_simvastatin__J069.log
• contingency_simvastatin__J069.tsv
• contingency_simvastatin__J841.tsv
• contingency_simvastatin__prescribed.tsv
• contingency_simvastatin__R13.tsv
• contingency_table.py
• contingency_test.log
• contingency_tramadol__F419.tsv
• contingency_tramadol__G473.tsv
• contingency_tramadol__K20.tsv
• contingency_tramadol__L409.tsv
• contingency_warfarin__optimal_dose.tsv
• contingency_warfarin__prescribed.tsv
• contingency_warfarin__R51.tsv
• contingency_zopiclone__G470.log
• contingency_zopiclone__G470.tsv
• contingency_zopiclone__M796.log
• contingency_zopiclone__M796.tsv
• contingency_zopiclone__M796_full.log
• covar/
• extract_phenotype.py
• filtered/
• generate_qc_plots.sh
• gwas_analyses_manual.md
• gwas_analysis_summary.tsv
• gwas_analysis_summary.tsv.bak.20260325_210511
• gwas_analysis_summary_backup.tsv
• gwas_analysis_summary_v2.tsv
• GWAS_DATA_SOURCES.md
• gwas_orchestrator.log
• gwas_orchestrator.log.bak.20260212_000657
• gwas_orchestrator.sh
• gwas_qc_summary.tsv
• gwas_viz.R
• gwas_viz_combined.R
• install_biomart.R
• install_deps.R
• locus_zoom_cyp2d6.R
• logs/
• logs_qc/
• manhattan.sh
• never_submitted_phenotypes_stats.tsv
• phenotypes_never_submitted.csv
• phenotypes_without_results.csv
• prescription_phenotypes-columns.csv
• prescriptions_phenotypes_stats.tsv
• progress.txt
• progress.txt.bak.20260212_000652
• qc_orchestrator.log
• qc_orchestrator.sh
• QC_PIPELINE.md
• qc_progress.txt
• qc_test/
• README.md
• recalc_summary.R
• regen_qc_plots.sh
• result/
• run_contingency.sh
• run_optimal_dose_regenie_dosages.sh
• run_tramadol_regenie_dosages.sh
• run_warfarin_regenie_dosages.sh
• runid/
• runs.txt
• serve.sh
• stop.sh
• submit_all_contingency.sh
• template-covar.json
• tests.md
• tramadol_phenotypes.txt
• venv/
• warfarin_regenie_dosages.tsv